Class 19: Cancer Mutation

Yane Lee PID A17670350

I downloaded my sequence form the class website and moved it tto my working directory:

From a BLASTp search against human refseq I see that it is:

-Official Symbol: TP53 -Official Full Name: tumor protein 53

library(bio3d)

a <- read.fasta("A17670350_mutant_seq.fa")
read.fasta("A17670350_mutant_seq.fa")

               1        .         .         .         .         .         60 
wt_healthy     MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP
mutant_tumor   MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP
               ************************************************************ 
               1        .         .         .         .         .         60 

              61        .         .         .         .         .         120 
wt_healthy     DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAK
mutant_tumor   DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYVGSYGERLGFLHSGTAK
               ******************************************* **** *********** 
              61        .         .         .         .         .         120 

             121        .         .         .         .         .         180 
wt_healthy     SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHE
mutant_tumor   SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHE
               ************************************************************ 
             121        .         .         .         .         .         180 

             181        .         .         .         .         .         240 
wt_healthy     RCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNS
mutant_tumor   RCSDSDGLAPPRHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNS
               *********** ************************************************ 
             181        .         .         .         .         .         240 

             241        .         .         .         .         .         300 
wt_healthy     SCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP
mutant_tumor   YCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP
                *********************************************************** 
             241        .         .         .         .         .         300 

             301        .         .         .         .         .         360 
wt_healthy     PGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPG
mutant_tumor   PGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPG
               ************************************************************ 
             301        .         .         .         .         .         360 

             361        .         .         .  393 
wt_healthy     GSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
mutant_tumor   GSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
               ********************************* 
             361        .         .         .  393 

Call:
  read.fasta(file = "A17670350_mutant_seq.fa")

Class:
  fasta

Alignment dimensions:
  2 sequence rows; 393 position columns (393 non-gap, 0 gap) 

+ attr: id, ali, call

We could score residue conservation

mutation.sites <- which(conserv(a) < 1)

paste(a$ali[1, mutation.sites],
mutation.sites,
a$ali[2, mutation.sites])

[1] "Q 104 V" "F 109 E" "Q 192 R" "S 241 Y"